[EMBOSS] water/needle interpreting swiss-format protein sequence files as DNA

[john walshaw (JIC)]

Hello,

If I create two swiss-format protein sequence files by using seqret on
an EMBOSS protein sequence DB, then use these two files as the input to
water or needle, I have to use "-sprotein1 -sprotein2" - otherwise they
are treated as DNA sequences.

In older versions of EMBOSS the files would automatically be treated as
protein - I tried this out with a few legacy installations and the need
to force the sequences to be protein appears to have been introduced in
4.1.0. I first noticed this problem when using 5.0.0, but version 4.0.0
automatically recognizes them as protein.

Is this intentional? (i.e. to ensure that DNA sequences with lots of
ambiguity codes don't get misinterpreted as protein).

If not, then I'll post full details.

best wishes,

John Walshaw

Department of Computational & Systems Biology
John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH,   UK